ADL: MOLKIT module pf Autodock tools

[Jeff Saxon]

Dear all,
I am looking for customization of Autodock-Tools scripts, which is
used for clusterization of conformations. This is a part of ADT
script, working with the directory of DLG filles, using Read module of
MolKit package:

    #read all the docking logs in as one Docking
    dlg_list = glob.glob(directory + '/*.dlg')
    d = Docking()
    for dlg in dlg_list:
        d.readDlg(dlg)
        if len(d.ch.conformations)>=500:
            print 'stop reading dlgs at', len(d.ch.conformations)
            break
    mol = d.ligMol
    crds = mol.AllAtoms.coords[:]
    d.clusterer.rmsTool = RMSDCalculator(crds)

how to change the subset of atoms (crds = mol.AllAtoms.coords) for
which RMSD is computed ? For instance, if I need to specify only
carbon atoms of the ligand or otherwise Centre of mass of all the
residue ?

Thank you in advance